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In 1655 the canton of Schwyz, which had elected to remain Catholic in 1531, began prosecuting those Protestant families who had remained in Schwyz. Some were turned in to the inquisition in Milan, some were beheaded, and the property of those who fled to Protestant Zurich was confiscated. Zurich demanded compensation for this property. Schwyz demanded the return of the refugees. Zurich urged Bern to declare war on the Catholic cantons (Schwyz and its allies Uri, Unterwalden, Zug and Lucerne).[1][2]

Zurich's forces lay in a fruitless siege of Rapperswil while Catholic forces separated Zurich from Bern, beating the Bernese at Villmergen on 24 January 1656. Hostilities ceased on 20 February and the treaty of Villmergen of 7 March reinstalled the status quo preceding the outbreak of hostilities, wherein each canton could specify the religion of all its residents.

Protestant resentment of the Catholic cantons grew as their own wealth, numbers and power grew, but their representation in the diet did not. Two votes for each canton assured the seven Catholic cantons political control over the four Protestant members (Two others were bi-confessional). Wars nearly broke out again in 1664, 1694 and 1697.

The abbot of St. Gallen proposed to build a "Catholic" road from Schwyz to Austria that would cut off the Protestant part of Glarus from its support in Zurich. In 1712 the abbot ordered the free inhabitants of Wattwil in the Toggenburg district to work on this road in spite of their having long ago been relieved of such a duty.

The rest of the district rose against the abbot, who refused to arbitrate, and blockaded his monasteries. Bern and Zurich declared war on the abbot who fled to Germany. The Protestants took Baden and started blockading the Catholic cantons. At peace negotiations in July, Lucerne and Uri were ready to reach an agreement, and the soldiers started to go home, but the pope renounced the terms and the Catholics renewed their attacks.[1]

This time, in the Toggenburg War, also called the Second War of Villmergen, after the decisive battle again fought near Villmergen, on 24 July, the Protestant side was successful.

The peace of Aarau (11 August 1712) brought more equality in religion, and thus an end to Catholic hegemony in the Swiss Confederation, staying the conflict until the renewed outbreak of civil war in 1847, the Sonderbundskrieg that led to the formation of Switzerland as a federal state.

The abbot eventually granted more religious freedom to the Toggenburg.[1] Both Bernese and Zurich troops took booty from the Abbey Library of St. Gall. While Berne later returned their share, Zurich only returned part of the goods, while a number of manuscripts as well as a large astronomical globe remain in possession of the canton of Zurich. In the 2000s, the canton of St. Gallen prepared for a court case to claim these back, while Zurich held that ownership had long been passed to the canton of Zurich. The parties agreed to attempt mediation rather than confrontation in court, a possibility for the solution of intercantonal disputes envisaged in the Swiss Federal Constitution of 2000. In the first case of such a mediation, led by Pascal Couchepin, the cantons found an amicable compromise. The ownership of the objects in question remains with Zurich, but a number of manuscripts are given as long-term loans to St. Gallen. The globe remains in the Landesmuseum in Zurich, but the canton of Zurich will manufacture an exact copy, and present this to St. Gallen as a gift.